The 50-year-old Beane rebuilt an A's team that made one of baseball's most surprising turnarounds in years, winning the American League West.
Beane, whose A's surprised the baseball world with a late-season surge that saw them win the American League West title, was presented the award on Wednesday night at the annual GM meetings which are underway in Indian Wells. The 50-year-old general manager also won the award following the 1999 season.
Following a 74-88 finish in 2011, Beane retooled Oakland's roster, trading pitchers Gio Gonzalez, Trevor Cahill and Andrew Bailey in exchange for several players who played key roles in the team's improbable campaign. The A's posted the best record in baseball after June 1 with a 72-38 mark, and overtook a heavily-favored Texas Rangers squad to win the AL West on the final day of the 2012 season.
Beane garnered 31 votes, while Washington Nationals general manager Mike Rizzo finished second with 13 votes. Jon Daniels of the Rangers finished third with six votes.